Rhombic dodecahedral (RD) Fe3O4 nanocrystals (NCs) were for the first time prepared via a rapid and facile microwave-assisted route in the presence of ionic liquids (ILs). The reaction could be finished within 15 min at temperatures as low as 90 °C. A proper amount of ILs played a key role in the synthesis of pure RD Fe3O4 NCs. In addition, the HMT-to-phenol molar ratio was also crucial for the growth of the RD Fe3O4 NCs. The phase structures, morphologies, and sizes of as-prepared products were investigated in detail by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and high-resolution TEM (HRTEM). The magnetic study reveals that the TB of the RD Fe3O4 NCs is found to be at 120 K, and the saturation magnetization is 86 emu g−1 at room temperature.